missingGenotypeRate: Missing genotype rate

In smgogarten/SeqVarTools: Tools for variant data

Missing genotype rate

Description

Calculate missing genotype rate by variant or by sample

Usage

## S4 method for signature 'SeqVarGDSClass'
missingGenotypeRate(gdsobj, margin=c("by.variant", "by.sample"), use.names=FALSE,
    parallel=FALSE)

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
margin	Possible values are "by.variant" or "by.sample," indicating whether the calculation should be done over all samples for each variant, or over all variants for each sample.
use.names	A logical indicating whether to assign variant IDs as names of the output vector.
parallel	Logical, numeric, or other value to control parallel processing; see seqParallel for details.

Details

Calculates the fraction of missing genotypes in a GDS object, either by variant or by sample.

Value

A numeric vector of missing genotype rates. If margin="by.variant", the vector will have length equal to the number of variants in the GDS object. If margin="by.sample", the vector will have length equal to the number of samples.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, applyMethod, getGenotype

Examples

gds <- seqOpen(seqExampleFileName("gds"))
head(missingGenotypeRate(gds, margin="by.variant"))
head(missingGenotypeRate(gds, margin="by.sample"))
seqClose(gds)

smgogarten/SeqVarTools documentation built on Sept. 15, 2024, 1:08 p.m.